Article
Plant Sciences
Sarah E. Flannery, Christopher Hepworth, William H. J. Wood, Federica Pastorelli, Christopher N. Hunter, Mark J. Dickman, Philip J. Jackson, Matthew P. Johnson
Summary: This study investigated the changes in thylakoid protein levels during long-term acclimation of Arabidopsis to different light intensities and found correlations with key photosynthetic parameters. High light promoted improved photosynthetic capacity and cyclic electron transport, while low light favored slowly reversible non-photochemical quenching. The data provide insights into how Arabidopsis tunes photosynthetic electron transfer and its regulation during developmental acclimation to light intensity.
Article
Plant Sciences
Fang Huang, Arturas Grauslys, Tuomas Huokko, Eva Caamano Gutierrez, Andrew R. Jones, Lu-Ning Liu
Summary: This study provides an in-depth statistical analysis of protein components and functionally linked complexes during cyanobacterial thylakoid membrane biogenesis. The findings reveal significant variations in abundance of photosystems, light-harvesting antennae, ABC transporters, and oxidative stress response and protein folding pathway enzymes between high light and growth light conditions. The results and analytical methodologies developed in this study may be valuable for studying global responses of thylakoid membrane biogenesis in plants and algae.
Article
Biochemistry & Molecular Biology
Adrian Cordido, Marta Vizoso-Gonzalez, Laura Nunez-Gonzalez, Alberto Molares-Vila, Maria del Pilar Chantada-Vazquez, Susana B. Bravo, Miguel A. Garcia-Gonzalez
Summary: This study used quantitative proteomics based on SWATH-MS technology to compare the hepatic proteomes of wild type and mutant/polycystic livers in a polycystic kidney disease (PKD) mouse model. Several proteins with altered abundance were identified, with a significant association with hepatic cystogenesis. Further analysis revealed a cluster focused on hepatic fibrinogens. Validation of selected targets confirmed their correlation with the quantitative proteomics data, validating the fibrinogen complex.
Article
Biochemistry & Molecular Biology
Paulina Czaplewska, Aleksandra E. Bogucka, Natalia Musial, Dmitry Tretiakow, Andrzej Skorek, Dominik Stodulski
Summary: The study aimed to explore protein components of human submandibular gland sialoliths matrix. Qualitative analysis was carried out using FASP methodology. By analyzing fragmentation spectra and using PEAKS Studio program, 254 human proteins and 393 bacterial proteins were identified in the sialolith extracts. The SWATH methodology was successfully applied for relative quantitative analysis of human proteins in deposits, providing a basis for further research.
Article
Virology
Michael Belshan, Alexander Holbrook, Joseph W. George, Hannah E. Durant, Michael Callahan, Spencer Jaquet, John T. West, Jacob Siedlik, Pawel Ciborowski
Summary: The study identified candidate biomarkers of latency in HIV-infected cells by comparing the membrane proteomes of latently infected Jurkat cell lines. Several proteins with significantly altered expression were found, with three factors showing consistent changes across multiple cell lines. The variable expression of most biomarkers across different cell clones suggests a multiplex approach may be needed for universal detection of latently infected cells.
Article
Biochemistry & Molecular Biology
Satoshi Hirano, Ryohei Goto, Yasuo Uchida
Summary: This study developed a comprehensive method to determine the localization of apical and basolateral membrane proteins, and applied it to analyze mouse liver proteome. The method successfully distinguished different membrane-localized proteins and revealed the differential protein expression between apical and basolateral membranes.
Article
Ophthalmology
Maite Lopez-Lopez, Uxia Regueiro, Susana B. Bravo, Maria del Pilar Chantada-Vazquez, Ruben Varela-Fernandez, Paulo Avila-Gomez, Pablo Hervella, Isabel Lema
Summary: Utilizing SWATH-MS for tear protein quantification, dysregulated proteins involved in iron homeostasis, inflammatory-immune response, oxidative stress, and other biological processes were identified in patients with keratoconus. The study sheds light on the molecular mechanisms underlying the disease and highlights the potential therapeutic targets related to iron accumulation and tissue damage in keratoconus pathophysiology.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2021)
Article
Environmental Sciences
Cong-Cong Shen, Mo-Xian Chen, Tian Xiao, Cheng Zhang, Jun Shang, Kai-Lu Zhang, Fu-Yuan Zhu
Summary: The study utilized SWATH-MS technology to analyze the proteome changes in poplar seedling roots following Pb treatment. Results showed that the lignin and flavonoid biosynthesis pathways were activated upon Pb exposure, while cell wall-related proteins exhibited increased abundances. Glutathione metabolism pathway may play a protective role in mitigating Pb-induced oxidative damages.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Article
Biochemistry & Molecular Biology
Jingfang Bian, Ying-Hon Sze, Dennis Yan-Yin Tse, Chi-Ho To, Sally A. McFadden, Carly Siu-Yin Lam, King-Kit Li, Thomas Chuen Lam
Summary: Most of the previous myopic animal studies used lower resolution proteomics approaches and single-candidate methods, making it difficult to detect minor changes. This study utilized SWATH proteomic analysis to identify significant protein changes in pigmented guinea pigs after induced myopia, highlighting lipid metabolism as a top function associated with differentially expressed proteins. The study provides new insights for further research in myopia control.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Sarah E. Flannery, Federica Pastorelli, Thomas Z. Emrich-Mills, Stuart A. Casson, C. Neil Hunter, Mark J. Dickman, Philip J. Jackson, Matthew P. Johnson
Summary: Plants adjust photosynthetic protein abundance to changing light intensity, but plants lacking STN7 gene still experience high PSII redox pressure in low light conditions.
Article
Plant Sciences
Jayendra Pandey, Elsinraju Devadasu, Deepak Saini, Kunal Dhokne, Sureshbabu Marriboina, Agepati. S. S. Raghavendra, Rajagopal Subramanyam
Summary: This study found that the effects of drought on photosynthesis have been extensively studied, but the effects on thylakoid organization are limited. The research observed a significant decline in gas exchange parameters and a reduction of photochemical efficiency of photosystem II and I in pea leaves under progressive drought stress. Furthermore, the study found changes in the organization of light-harvesting complexes and reductions in supercomplexes of thylakoids in drought-affected plants.
Article
Plant Sciences
Kunal Dhokne, Jayendra Pandey, Ranay Mohan Yadav, Pavithra Ramachandran, Jyoti Ranjan Rath, Rajagopal Subramanyam
Summary: Salt stress has adverse effects on the photosynthetic process and thylakoid structure in Pea. Under high salt conditions, the net photosynthetic rate decreases, water use efficiency improves, and the photochemical efficiency of both photosystems is reduced. Non-photochemical quenching is decreased, while non-regulated energy dissipation increases, leading to the inactivation of PSII. Salt stress also affects the electron transport chain, causing disorganization of thylakoid grana and altering the macro-organization and super complexes of thylakoids.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2022)
Article
Agronomy
Magdalena Serafin-Andrzejewska, Marcin Kozak, Andrzej Kotecki
Summary: Pod sealant application has a positive impact on the quantity and quality traits of field peas, improving traits such as number of pods per plant, seed weight per pod, seed yield, protein content in seeds, and total protein productivity. However, the effect on number of seeds per pod is not significant, and the interaction between cultivar and pod sealant application showed significant effects on certain traits in 2019.
Review
Environmental Sciences
Sanghamitra Majumdar, Arturo A. Keller
Summary: With increasing global food demand and risks associated with climate change and agrochemicals, novel and sustainable agricultural practices are needed to improve crop yield and quality. Nanotechnology strategies have been explored widely, but limited understanding of nanomaterial safety constrains their application in the food industry. Interest in the potential of engineered nanomaterials in agricultural applications has led to increased crop exposure, posing unknown risks to plants, animals, and humans.
CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY
(2021)
Review
Genetics & Heredity
Rajib Roychowdhury, Soumya Prakash Das, Amber Gupta, Parul Parihar, Kottakota Chandrasekhar, Umakanta Sarker, Ajay Kumar, Devade Pandurang Ramrao, Chinta Sudhakar
Summary: Global warming and climate change have negative effects on plants by imposing environmental stresses and disease pressure. Multi-omics approaches, including genomics, transcriptomics, proteomics, metabolomics, etc., have become useful tools to understand plant responses to abiotic stress and develop climate-smart crops.
Article
Biotechnology & Applied Microbiology
Beatrice Mongili, Annalisa Abdel Azim, Silvia Fraterrigo Garofalo, Esperanza Batuecas, Angela Re, Sergio Bocchini, Debora Fino
Summary: This study explores the use of DMC for PHB extraction, and investigates different experimental conditions to optimize extraction performance. Comparisons between PHB extracted using DMC and chloroform show that DMC/ethanol is a more environmentally friendly and health-conscious choice.
BIOTECHNOLOGY FOR BIOFUELS
(2021)
Article
Cell Biology
Denise Sighel, Michela Notarangelo, Shintaro Aibara, Angela Re, Gianluca Ricci, Marianna Guida, Alessia Soldano, Valentina Adami, Chiara Ambrosini, Francesca Broso, Emanuele Filiberto Rosatti, Sara Longhi, Mariachiara Buccarelli, Quintino G. D'Alessandris, Stefano Giannetti, Simone Pacioni, Lucia Ricci-Vitiani, Joanna Rorbach, Roberto Pallini, Sandrine Roulland, Alexey Amunts, Ines Mancini, Angelika Modelska, Alessandro Quattrone
Summary: This study suggests that targeting mitochondrial translation could be a potential therapeutic strategy to suppress GSC growth in GBM. The bacterial antibiotic quinupristin/dalfopristin (Q/D) was found to effectively inhibit GSC growth by binding to the large mitoribosomal subunit, inhibiting mitochondrial protein synthesis, and disrupting OXPHOS complexes.
Article
Microbiology
Nicolo S. Vasile, Alessandro Cordara, Giulia Usai, Angela Re
Summary: This study focuses on biomass cultivation of cyanobacterial cell factories in photobioreactors, with particular emphasis on the impact of light intensity on cellular physiology and productivity, and proposes a modeling framework for predicting growth of the model organism under different light conditions. The analysis highlights the importance of constraining the model with light calibration and measurement data to enhance accuracy and extrapolation capabilities.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Paolo Costa, Giulia Usai, Angela Re, Marcello Manfredi, Giuseppe Mannino, Cinzia Margherita Bertea, Enrica Pessione, Roberto Mazzoli
Summary: Comparative gel-free proteomics analysis of Clostridium cellulovorans exposed to butanol revealed modulation of protein biosynthesis, up-regulation of ATPases, and rearrangement of cell envelope, suggesting potential gene targets for metabolic engineering strategies aimed at improving butanol tolerance in this microbial strain.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Plant Sciences
Beatrice Battaglino, Alessandro Grinzato, Cristina Pagliano
Summary: This study investigated the inhibitory effects of several PSII-inhibiting herbicides on plant PSII, revealing some of them have a high affinity for the D1 Q(B) site, which could provide valuable information for the future design of more selective herbicides.
Article
Biophysics
Stefania Lettieri, Beatrice Battaglino, Adriano Sacco, Guido Saracco, Cristina Pagliano
Summary: This study presents an easy-to-assemble amperometric electrochemical biosensor incorporating thylakoid membranes for the detection of photosynthetic herbicides, achieving high photocurrents, long storage stability, reproducible detections, and good sensitivity. The biosensor showed a half-life longer than 15 days at 4 degrees C and full stability up to 4 months at -80 degrees C.
BIOSENSORS & BIOELECTRONICS
(2022)
Article
Biochemical Research Methods
Beatrice Battaglino, Wei Du, Cristina Pagliano, Joeri A. Jongbloets, Angela Re, Guido Saracco, Filipe Branco dos Santos
Summary: Cyanobacteria, powered by sunlight, have the potential to convert atmospheric CO2 into valuable compounds while releasing O2, making them promising candidates for microbial cell factories. By utilizing growth-coupled metabolites and thermodynamically favored conversions, the scope of candidate compounds for production can be expanded, leading to increased stability and productivity of engineered strains.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Microbiology
Parsa Ghadermazi, Angela Re, Luca Ricci, Siu Hung Joshua Chan
Summary: Gas fermentation is a promising method to convert low-cost waste gases into valuable chemicals. This study used modeling and kinetic ensemble modeling to analyze metabolic engineering interventions for increased 2,3-butanediol production and reduced carbon loss. The results suggested that interventions targeting by-products branching from acetyl-CoA and pyruvate are effective strategies.
Article
Microbiology
Pier Francesco Di Leonardo, Giacomo Antonicelli, Valeria Agostino, Angela Re
Summary: Understanding the organizational and functional properties of hydrogen metabolism is crucial for creating a framework to support a hydrogen-fueled low-carbon economy. This study investigated the genomes of several industrially relevant acetogens and identified their hydrogenases' repertoire. The findings provide valuable knowledge on the functional specificity and potential applications of hydrogenases in biotechnological processes.
MICROBIOLOGY SPECTRUM
(2022)
Review
Biotechnology & Applied Microbiology
Angela Re, Roberto Mazzoli
Summary: The fermentative production of n-butanol has regained interest in recent decades due to its use as a drop-in fuel. Utilizing lignocellulose as a feedstock can increase economic competitiveness, but its high recalcitrance requires pre-treatment and multiple processes. Strategies for developing microbial strains for efficient cellulose depolymerization and butanol production are discussed, along with the challenge of butanol toxicity and strategies for developing tolerant strains.
MICROBIAL BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Giulia Usai, Alessandro Cordara, Angela Re, Maria Francesca Polli, Giuseppe Mannino, Cinzia Margherita Bertea, Debora Fino, Candido Fabrizio Pirri, Barbara Menin
Summary: This study improves the production performance of 2-Phenylethanol (2-PE) in the Synechococcus elongatus PCC 7942 p120 strain through metabolite doping and metabolic engineering, resulting in significantly increased yield and concentration of 2-PE.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Luca Ricci, Arne Seifert, Sebastien Bernacchi, Debora Fino, Candido Fabrizio Pirri, Angela Re
Summary: Gas fermentation technology can convert carbon dioxide into valuable chemicals, playing an important role in the development of circular carbon economy. This review presents the potential applications of gas fermentation technology and its integration with other biotechnological processes, demonstrating its versatility and significance in various production processes.
MICROBIAL BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Johannes F. Hevler, Pascal Albanese, Alfredo Cabrera-Orefice, Alisa Potter, Andris Jankevics, Jelena Misic, Richard A. Scheltema, Ulrich Brandt, Susanne Arnold, Albert J. R. Heck
Summary: The tricarboxylic acid cycle is a central pathway for energy production in eukaryotic cells and plays a key role in aerobic respiration across all life kingdoms. The 2-oxoglutarate dehydrogenase complex (OGDHC) is a crucial enzyme in this cycle, generating NADH by oxidatively decarboxylating 2-oxoglutarate to succinyl-CoA. We provide evidence that MRPS36 is an important component of eukaryotic OGDHC, supported by cross-linking mass spectrometry data and phylogenetic analyses. We propose that MRPS36 evolved as an E3 adaptor protein, functionally replacing the peripheral subunit-binding domain (PSBD) in eukaryotic E2o.
Article
Chemistry, Multidisciplinary
Loredana Tarraran, Valeria Agostino, Nicolo S. Vasile, Annalisa Abdel Azim, Giacomo Antonicelli, Jonathan Baker, James Millard, Angela Re, Barbara Menin, Tonia Tommasi, Nigel P. Minton, Candido F. Pirri, Debora Fino
Summary: Global warming has led to the development of strategies that utilize CO2 as raw material to produce compounds for industry. This study modified Acetobacterium woodii to convert CO2 and H2 into acetone through gas fermentation. The research investigated the catalytic performance of the modified strain under high pressure conditions and found that growth inhibition and formic acid production were due to bicarbonate build-up in the reactor at high CO2 partial pressure.
JOURNAL OF CO2 UTILIZATION
(2023)
Article
Biotechnology & Applied Microbiology
Luca Ricci, Valeria Agostino, Debora Fino, Angela Re
Summary: Gas fermentation by acetogens of the genus Clostridium is a promising technology for producing biochemicals and biofuels from industrial waste gases. Among acetogenic organisms, C. ljungdahlii shows higher efficiency in producing 2,3-butanediol compared to C. autoethanogenum. The presence of mineral elements Zinc and Iron has a significant positive influence on the titer and productivity of 2,3-butanediol.
FERMENTATION-BASEL
(2021)